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migrate changes to Cell Ranger module tests from UniverSC PR #2646

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Merged
merged 2 commits into from
Jan 18, 2023
Merged

migrate changes to Cell Ranger module tests from UniverSC PR #2646

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e856e62
migrate changes to Cell Ranger module tests from
Dec 13, 2022
a99d80f
Merge branch 'master' of ssh://github.com/nf-core/modules into cellra…
Jan 18, 2023
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2 changes: 1 addition & 1 deletion tests/modules/nf-core/cellranger/count/nextflow.config
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Expand Up @@ -25,7 +25,7 @@ process {
}

withName: CELLRANGER_COUNT {
ext.args = '--chemistry SC3Pv3'
ext.args = '--chemistry SC3Pv3 --description sample-123'
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Suggested change
ext.args = '--chemistry SC3Pv3 --description sample-123'
ext.args = '--chemistry SC3Pv3'

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I did not see the param you proposed in the cellranger docs:
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count

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It's documented in the command-line help system.

$ cellranger count --help
cellranger-count
Count gene expression (targeted or whole-transcriptome) and/or feature barcode reads from a single sample and GEM well

USAGE:
    cellranger count [OPTIONS] --id <ID> --transcriptome <PATH>

OPTIONS:
        --id <ID>                                     A unique run id and output folder name [a-zA-Z0-9_-]+
        --description <TEXT>                          Sample description to embed in output files [default: ]

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@TomKellyGenetics TomKellyGenetics Dec 16, 2022 •
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For context this returns a string in the web_summary.html file so the reason I implemented this was to:

a. match results between Cell Ranger and UniverSC tests with 10X Genomics data.
b. enable unit testing with a "contain" check (which passes locally but was removed during review of GitHub Actions results)

As discussed here: #1706 (comment)

}

}
9 changes: 3 additions & 6 deletions tests/modules/nf-core/cellranger/count/test.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
- name: cellranger count test_cellranger_count
command: nextflow run ./tests/modules/nf-core/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/count/nextflow.config
command: nextflow run ./tests/modules/nf-core/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/count/nextflow.config
tags:
- cellranger/count
- cellranger
Expand Down Expand Up @@ -35,17 +35,13 @@
- path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
md5sum: 02a8f4575bdfcd4a42b4d8d07f2e9369
- path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
contains: ["genomeGenerate"]
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
- path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
md5sum: cedcb5f4e7d97bc548cd5daa022e092c
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
md5sum: f8b6b7cc8248151a98c46d4ebec450c6
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
- path: output/cellranger/sample-123/outs/metrics_summary.csv
md5sum: 707df0f101d479d93f412ca74f9c4131
- path: output/cellranger/sample-123/outs/molecule_info.h5
Expand All @@ -63,3 +59,4 @@
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
md5sum: bdce94a51f16e22d40301724080b76ee
- path: output/cellranger/sample-123/outs/web_summary.html
contains: ["sample-123"]
2 changes: 1 addition & 1 deletion tests/modules/nf-core/cellranger/mkgtf/test.yml
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@@ -1,5 +1,5 @@
- name: cellranger mkgtf test_cellranger_mkgtf
command: nextflow run ./tests/modules/nf-core/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkgtf/nextflow.config
command: nextflow run ./tests/modules/nf-core/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkgtf/nextflow.config
tags:
- cellranger/mkgtf
- cellranger
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3 changes: 2 additions & 1 deletion tests/modules/nf-core/cellranger/mkref/test.yml
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@@ -1,5 +1,5 @@
- name: cellranger mkref test_cellranger_mkref
command: nextflow run ./tests/modules/nf-core/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkref/nextflow.config
command: nextflow run ./tests/modules/nf-core/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cellranger/mkref/nextflow.config
tags:
- cellranger/mkref
- cellranger
Expand Down Expand Up @@ -33,6 +33,7 @@
- path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
contains: ["genomeGenerate"]
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
Expand Down